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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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147 new terms added for new Food packages #201

Closed only1chunts closed 3 years ago

only1chunts commented 3 years ago

All the terms listed below have been approved for inclusion in the new "Food" package to be included in v6. I am adding this list here to enable a history of the new terms to be included in the repo and the change log.

If anyone spots anything that needs to be looked at please create a new GitHub ticket specifically for the Term in question.

Of note:

Term name - growth medium
Structured comment name - growth_medium
Definition - A liquid or gel containing nutrients, salts, and other factors formulated to support the growth of microorganisms, cells, or plants (National Cancer Institute Thesaurus).  The name of the medium used to grow the microorganism.
Expected value - text
Value syntax - {text}
Example - LB broth
Term ID - MIXS:0001108
Package(s) - Food
Term name - farm watering water source
Structured comment name - farm_water_source
Definition - Source of water used on the farm for irrigation of crops or watering of livestock.
Expected value - enumeration
Value syntax - [freshwater|brackish|saline|natural|manmade|estuary|lake|pond|canal|stream|river|melt pond|well|ditch|reservior|collected rainwater|municipal|storage tank]
Example - water well (ENVO:01000002)
Term ID - MIXS:0001110
Package(s) - Food
Term name - plant water delivery method
Structured comment name - plant_water_method
Definition - Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes.
Expected value - AGRO_00000006
Value syntax - {termLabel} {[termID]}
Example - drip irrigation process [AGRO:00000056]
Term ID - MIXS:0001111
Package(s) - Food
Term name - air particulate matter concentration
Structured comment name - air_PM_concen
Definition - Concentration (micrograms per cubic meter) of fine solid or liquid particles carried by the air, including particulate matter size fraction. Multiple terms can be separated by pipes.
Expected value - enumeration; measurement value
Value syntax - [PM 0.1|PM 10|PM 2.5]; {measurement value}
Example - PM 0.1; 37 micrograms per cubic meter
Term ID - MIXS:0001112
Package(s) - Food

See ticket #213 - is air_pm_concen different to resp_part_matter?

Term name - animal feeding equipment
Structured comment name - animal_feed_equip
Definition - Description of the feeding equipment used for livestock. This field accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757). Multiple terms can be separated by one or more pipes.
Expected value - EOL:0001757
Value syntax - {termLabel} {[termID]}
Example - self feeding [EOL:0001645]| straight feed trough [EOL:0001661]
Term ID - MIXS:0001113
Package(s) - Food
Term name - animal intrusion near sample source
Structured comment name - animal_intrusion
Definition - Identification of animals intruding on the sample or sample site including invertebrates (such as pests or pollinators) and vertebrates (such as wildlife or domesticated animals). This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.
Expected value - NCIT:C14250 or NCBI taxid
Value syntax - {termLabel} {[termID]}|{integer}
Example - Thripidae [NCBITaxon:45053]
Term ID - MIXS:0001114
Package(s) - Food
Term name - animal water delivery method
Structured comment name - anim_water_method
Definition - Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes.
Expected value - EOL_0001653
Value syntax - {termLabel} {[termID]}
Example - water trough [EOL:0001618]
Term ID - MIXS:0001115
Package(s) - Food
Term name - crop yield
Structured comment name - crop_yield
Definition - Amount of crop produced per unit or area of land.
Expected value - measurement value
Value syntax - {float}{unit}
Example - 570 kilogram per metre square
Term ID - MIXS:0001116
Package(s) - Food

Should the description of crop_yield include something to describe how this value is linked to the sampled item? e.g. is this the yield from crop grown on the site sampled, or the yield of the sampled plant crop or something else?

Term name - culture result
Structured comment name - cult_result
Definition - Any result of a bacterial culture experiment reported as a binary assessment such as positive/negative, active/inactive.
Expected value - enumeration
Value syntax - [absent|active|inactive|negative|no|present|positive|yes]
Example - positive
Term ID - MIXS:0001117
Package(s) - Food

Description needs to include link to cult_result_org as both fields are required to make any sense of this value.

Term name - culture result organism
Structured comment name - cult_result_org
Definition - Taxonomic information about the cultured organism(s).
Expected value - NCIT:C14250 or NCBI taxid
Value syntax - {termLabel} {[termID]}|{integer}
Example - Listeria monocytogenes [NCIT:C86502]
Term ID - MIXS:0001118
Package(s) - Food

see above term.

Term name - culture target microbial analyte
Structured comment name - cult_target
Definition - The target microbial analyte in terms of investigation scope. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
Expected value - NCIT:C14250 or NCBI taxid or culture independent
Value syntax - {termLabel} {[termID]}|{integer}
Example - Listeria monocytogenes [NCIT:C86502]
Term ID - MIXS:0001119
Package(s) - Food
Term name - degree of plant part maturity
Structured comment name - plant_part_maturity
Definition - A description of the stage of development of a plant or plant part based on maturity or ripeness. This field accepts terms listed under degree of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050).
Expected value - FOODON:03530050
Value syntax - {term label}{term ID}
Example - ripe or mature [FOODON:03530052]
Term ID - MIXS:0001120
Package(s) - Food

again- how does this relate the thing actually sequenced

Term name - ecosystem(s) adjacent to farm
Structured comment name - adjacent_ecosystem
Definition - Description of the environmental features that are adjacent to the farm. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes.
Expected value - ENVO_01001110 or ENVO_00000070
Value syntax - {termLabel}{[termID]}
Example - estuarine biome [ENVO:01000020]
Term ID - MIXS:0001121
Package(s) - Food

see ticket #212 broaden the use of the term to be included in other packages

Term name - environmental feature adjacent water source
Structured comment name - water_source_adjac
Definition - Description of the environmental features that are adjacent to the farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes.
Expected value - ENVO_01001110 or ENVO_00000070
Value syntax - {text}
Example - feedlot [ENVO:01000627]
Term ID - MIXS:0001122
Package(s) - Food
Term name - equipment shared with other farms
Structured comment name - farm_equip_shared
Definition - List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes.
Expected value - AGRO:00000416
Value syntax - {termLabel} {[termID]}
Example - combine harvester [AGRO:00000473]
Term ID - MIXS:0001123
Package(s) - Food
Term name - farm equipment sanitization
Structured comment name - farm_equip_san
Definition - Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution.  Multiple terms can be separated by one or more pipes.
Expected value - text or commercial name of sanitizer or class of sanitizer or active ingredient in sanitizer
Value syntax - {text} {float} {unit}
Example - hot water pressure wash, hypochlorite solution, 50 parts per million
Term ID - MIXS:0001124
Package(s) - Food
Term name - farm equipment sanitization frequency
Structured comment name - farm_equip_san_freq
Definition - The number of times farm equipment is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
Expected value - text
Value syntax - {text}
Example - Biweekly
Term ID - MIXS:0001125
Package(s) - Food
Term name - farm equipment used
Structured comment name - farm_equip
Definition - List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season.  This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes.
Expected value - AGRO:00000416
Value syntax - {termLabel} {[termID]}
Example - combine harvester [AGRO:00000473]
Term ID - MIXS:0001126
Package(s) - Food
Term name - fertilizer administration
Structured comment name - fertilizer_admin
Definition - Type of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order.
Expected value - AGRO_00002062
Value syntax - {termLabel} {[termID]}
Example - fish emulsion [AGRO:00000082]
Term ID - MIXS:0001127
Package(s) - Food
Term name - fertilizer administration date
Structured comment name - fertilizer_date
Definition - Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order.
Expected value - date and time
Value syntax - {timestamp}
Example - 2018-05-11T10:00:00+01:00
Term ID - MIXS:0001128
Package(s) - Food
Term name - food animal group size
Structured comment name - animal_group_size
Definition - The number of food animals of the same species that are maintained together as a unit, i.e. a herd or flock.
Expected value - value
Value syntax - {integer}
Example - 80
Term ID - MIXS:0001129
Package(s) - Food
Term name - food animal source diet
Structured comment name - animal_diet
Definition - If the isolate is from a food animal, the type of diet eaten by the food animal.  Please list the main food staple and the setting, if appropriate.  For a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org.  Multiple terms may apply and can be separated by pipes |Food product for animal covers foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997. If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes. If the proper descriptor is not listed please use text to describe the food product type.
Expected value - FOODON:03309997
Value syntax - {text}
Example - Hay [FOODON:03301763]
Term ID - MIXS:0001130
Package(s) - Food
Term name - food contact surface
Structured comment name - food_contact_surf
Definition - The specific container or coating materials in direct contact with the food. Multiple values can be assigned.  This field accepts terms listed under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010).
Expected value - FOODON:03500010
Value syntax - {text}|{termLabel} {[termID]}
Example - cellulose acetate [FOODON:03500034]
Term ID - MIXS:0001131
Package(s) - Food
Term name - food container or wrapping
Structured comment name - food_contain_wrap
Definition - Type of container or wrapping defined by the main container material, the container form, and the material of the liner lids or ends. Also type of container or wrapping by form; prefer description by material first, then by form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100).
Expected value - FOODON:03490100
Value syntax - {text}|{termLabel} {[termID]}
Example - Plastic shrink-pack [FOODON:03490137]
Term ID - MIXS:0001132
Package(s) - Food
Term name - Food harvesting process
Structured comment name - food_harvest_proc
Definition - A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism.
Expected value - free text
Value syntax - {text}
Example - hand-picked
Term ID - MIXS:0001133
Package(s) - Food
Term name - food packing medium
Structured comment name - food_pack_medium
Definition - The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal.  This includes edible packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), vacuum packed, or packed with aerosol propellant. This field accepts terms under food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple terms may apply and can be separated by pipes.
Expected value - FOODON:03480020
Value syntax - {text}|{termLabel} {[termID]}
Example - vacuum-packed[FOODON:03480027]
Term ID - MIXS:0001134
Package(s) - Food
Term name - food preservation process
Structured comment name - food_preserv_proc
Definition - The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. This field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107).
Expected value - FOODON:03470107
Value syntax - {text}|{termLabel} {[termID]}
Example - food slow freezing [FOODON:03470128]
Term ID - MIXS:0001135
Package(s) - Food
Term name - food production characteristics
Structured comment name - food_prod_char
Definition - Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef.
Expected value - text
Value syntax - {text}
Example - wild caught
Term ID - MIXS:0001136
Package(s) - Food
Term name - food shipping transportation method
Structured comment name - food_trav_mode
Definition - A descriptor for the method of movement of food commodity along the food distribution system.  This field accepts terms listed under travel mode (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes.
Expected value - GENEPIO:0001064
Value syntax - {termLabel} {[termID]}
Example - train travel [GENEPIO:0001060]
Term ID - MIXS:0001137
Package(s) - Food
Term name - Food shipping transportation vehicle
Structured comment name - food_trav_vehic
Definition - A descriptor for the mobile machine which is used to transport food commodities along the food distribution system.  This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes.
Expected value - ENVO:01000604
Value syntax - {text}|{termLabel} {[termID]}
Example - aircraft [ENVO:01001488]|car [ENVO:01000605]
Term ID - MIXS:0001138
Package(s) - Food
Term name - food source
Structured comment name - food_source
Definition - Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995].
Expected value - FOODON
Value syntax - {termLabel} {[termID]}
Example - giant tiger prawn [FOODON:03412612]
Term ID - MIXS:0001139
Package(s) - Food
Term name - food treatment process
Structured comment name - food_treat_proc
Definition - Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. This fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111).
Expected value - FOODON:03460111
Value syntax - {text}|{termLabel} {[termID]}
Example - gluten removal process [FOODON:03460750]
Term ID - MIXS:0001140
Package(s) - Food
Term name - extreme weather event
Structured comment name - extr_weather_event
Definition - Unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order.
Expected value - enumeration
Value syntax - [drought|dust storm|extreme cold|extreme heat|flood|frost|hail|high precipitationhigh winds]
Example - hail
Term ID - MIXS:0001141
Package(s) - Food
Term name - extreme weather date
Structured comment name - date_extr_weath
Definition - Date of unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order.
Expected value - date
Value syntax - {timestamp}
Example - 2018-05-11:T14:30Z
Term ID - MIXS:0001142
Package(s) - Food
Term name - host variety or cultivar
Structured comment name - host_variety
Definition - The variety or cultivar of the host organism; the name given to a particular variety of organism to distinguish it from otherwise similar organisms of the same species.
Expected value - text
Value syntax - {text}
Example - romaine lettuce; Athena melons; Patio Snacker cucumbers
Term ID - MIXS:0001143
Package(s) - Food

see ticket #202 how is this different to "host subspecific genetic lineage" ?

Term name - intended consumer
Structured comment name - intended_consumer
Definition - Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid.
Expected value - FOODON_03510136 or NCBI taxid
Value syntax - {integer}|{termLabel} {[termID]}        
Example - 9606 o rsenior as food consumer [FOODON:03510254] 
Term ID - MIXS:0001144
Package(s) - Food
Term name - library preparation kit
Structured comment name - library_prep_kit
Definition - Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.
Expected value - name of library preparation kit
Value syntax - {text}
Example - Illumina DNA Prep
Term ID - MIXS:0001145
Package(s) - Food
Term name - local air flow impediments
Structured comment name - air_flow_impede
Definition - Presence of objects in the area that would influence or impede air flow through the air filter.
Expected value - enumeration;obstruction type; distance from sampling device
Value syntax - [obstructed|unobstructed]; {text}; {measurement value}
Example - obstructed;hay bales; 2 m
Term ID - MIXS:0001146
Package(s) - Food
Term name - lot number
Structured comment name - lot_number
Definition - A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number.  The submitter should provide lot number of the item followed by the item name for which the lot number was provided.
Expected value - lot number, item
Value syntax - {integer}, {text}
Example - 1239ABC01A, split Cornish hens
Term ID - MIXS:0001147
Package(s) - Food
Term name - mean seasonal humidity
Structured comment name - season_humidity
Definition - Average humidity of the region throughout the growing season.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 0.25
Term ID - MIXS:0001148
Package(s) - Food
Term name - part of plant or animal
Structured comment name - part_plant_animal
Definition - The anatomical part of the organism being involved in food production or consumption; e.g., a carrot is the root of the plant (root vegetable). This field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116).
Expected value - FOODON:03420116
Value syntax - {text}|{termLabel} {[termID]}
Example - chuck [FOODON:03530021]
Term ID - MIXS:0001149
Package(s) - Food
Term name - plant reproductive part
Structured comment name - plant_reprod_crop
Definition - Plant reproductive part used in the field during planting to start the crop.
Expected value - enumeration
Value syntax - [plant cutting|pregerminated seed|ratoon|seed|seedling|whole mature plant]
Example - seedling
Term ID - MIXS:0001150
Package(s) - Food
Term name - purpose of sampling
Structured comment name - samp_purpose
Definition - The reason that the sample was collected.
Expected value - enumeration or {text}
Value syntax - [active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|clinical trial|cluster investigation|environmental assessment|farm sample|field trial|for cause|industry internal investigation|market sample|passive surveillance|population based studies|research|research and development] or {text}
Example - field trial
Term ID - MIXS:0001151
Package(s) - Food
Term name - repository name
Structured comment name - repository_name
Definition - The name of the institution where the sample or DNA extract is held or sample not available if the sample was used in its entirety for analysis or otherwise not retained.
Expected value - Institution
Value syntax - {text}
Example - FDA CFSAN Microbiology Laboratories
Term ID - MIXS:0001152
Package(s) - Food
Term name - sample pooling
Structured comment name - samp_pooling
Definition - Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled.
Expected value - text
Value syntax - {text}
Example - 5uL of extracted genomic DNA from 5 leaves were pooled
Term ID - MIXS:0001153
Package(s) - Food
Term name - sample source material category
Structured comment name - samp_source_mat_cat
Definition - This is the scientific role or category that the subject organism or material has with respect to an investigation.  This field accepts terms listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237).
Expected value - GENEPIO:0001237
Value syntax - {termLabel} {[termID]}
Example - environmental (swab or sampling) [GENEPIO:0001732]
Term ID - MIXS:0001154
Package(s) - Food
Term name - sequencing kit
Structured comment name - sequencing_kit
Definition - Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. Indicate name of the sequencing kit.
Expected value - name of sequencing kit used
Value syntax - {text}
Example - NextSeq 500/550 High Output Kit v2.5 (75 Cycles)
Term ID - MIXS:0001155
Package(s) - Food
Term name - sequencing location
Structured comment name - sequencing_location
Definition - The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced.
Expected value - text
Value syntax - {text}
Example - University of Maryland Genomics Resource Center
Term ID - MIXS:0001156
Package(s) - Food
Term name - serovar or serotype
Structured comment name - serovar_or_serotype
Definition - A characterization of a cell or microorganism based on the antigenic properties of the molecules on its surface. Indicate the name of a serovar or serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
Expected value - NCIT:C14250 or NCBI taxid
Value syntax - {termLabel} {[termID]}|{integer}
Example - Escherichia coli strain O157:H7 [NCIT:C86883]
Term ID - MIXS:0001157
Package(s) - Food
Term name - soil conductivity
Structured comment name - soil_conductivity
Definition - Conductivity of soil at time of sampling.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 10 milliSiemens per centimeter
Term ID - MIXS:0001158
Package(s) - Food

We already have a term called "conductivity" the definition of which is restricted to water, but should we consider broadening that definition instead of creating a new term here?

Term name - soil cover
Structured comment name - soil_cover
Definition - Description of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material.
Expected value - ENVO:00010483
Value syntax - {termLabel} {[termID]}
Example - bare soil [ENVO01001616]
Term ID - MIXS:0001159
Package(s) - Food
Term name - soil pH
Structured comment name - soil_pH
Definition - The pH of soil at time of sampling.
Expected value - measurement value
Value syntax - {float}
Example - 7.2
Term ID - MIXS:0001160
Package(s) - Food
Term name - soil relative location
Structured comment name - soil_rel_location
Definition - Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road.
Expected value - text
Value syntax - {text}
Example - furrow
Term ID - MIXS:0001161
Package(s) - Food
Term name - soil sediment porosity
Structured comment name - soil_porosity
Definition - Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample.
Expected value - percent porosity
Value syntax - {percentage}
Example - 0.2
Term ID - MIXS:0001162
Package(s) - Food
Term name - soil temperature
Structured comment name - soil_temp
Definition - Temperature of soil at the time of sampling.
Expected value - measurement value
Value syntax - {float}{unit}
Example - 25 degrees Celsius
Term ID - MIXS:0001163
Package(s) - Food
Term name - soil texture classification
Structured comment name - soil_texture_class
Definition - One of the 12 soil texture classes use to describe soil texture based on the relative proportion of different grain sizes  of mineral particles [sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil.
Expected value - enumeration
Value syntax - [clay|clay loam|loam|loamy sand|sand|sandy clay|sandy clay loam|sandy loam|silt|silty clay|silty clay loam|silt loam]
Example - silty clay loam
Term ID - MIXS:0001164
Package(s) - Food

see ticket #214 - term already exist with different name in soil package.

Term name - soil texture method
Structured comment name - soil_texture_meth
Definition - Reference or method used in determining soil texture classification.
Expected value - PMID,DOI or url
Value syntax - {PMID}|{DOI}|{URL}
Example - https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf (hydrometer method)
Term ID - MIXS:0001165
Package(s) - Food

see ticket #214 - term already exist with different name in soil package.

Term name - soil type name
Structured comment name - soil_type_name
Definition - Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms can be separated by pipes.
Expected value - ENVO_00001998
Value syntax - {termLabel} {[termID]}
Example - plinthosol [ENVO:00002250]
Term ID - MIXS:0001166
Package(s) - Food

see ticket #214 - term already exist with different name in soil package.

Term name - spike in organism
Structured comment name - spikein_org
Definition - Taxonomic information about the spike-in organism(s). This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.
Expected value - NCIT:C14250 or NCBI taxid
Value syntax - {termLabel} {[termID]}|{integer}
Example - Listeria monocytogenes [NCIT:C86502]|28901
Term ID - MIXS:0001167
Package(s) - Food
Term name - spike-in bacterial serovar or serotype
Structured comment name - spikein_serovar
Definition - Taxonomic information about the spike-in organism(s) at the serovar or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.
Expected value - NCIT:C14250 or antigenic formula or serovar name
Value syntax - {termLabel} {[termID]}|{integer}
Example - Escherichia coli strain O157:H7 [NCIT:C86883]|83334
Term ID - MIXS:0001168
Package(s) - Food
Term name - spike-in growth medium
Structured comment name - spikein_growth_med
Definition - A liquid or gel containing nutrients, salts, and other factors formulated to support the growth of microorganisms, cells, or plants (National Cancer Institute Thesaurus).  A growth medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment.  In this case, list the culture medium used to propagate the spike-in bacteria during preparation of spike-in inoculum. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the spike in growth media.
Expected value - MICRO:0000067
Value syntax - {text}|{termLabel} {[termID]}
Example - LB broth [MCO:0000036]
Term ID - MIXS:0001169
Package(s) - Food
Term name - spike-in microbial strain
Structured comment name - spikein_strain
Definition - Taxonomic information about the spike-in organism(s) at the strain level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.
Expected value - NCIT:C14250 or NCBI taxid or text
Value syntax - {termLabel} {[termID]}|{integer}
Example - 169963
Term ID - MIXS:0001170
Package(s) - Food
Term name - spike-in with antibiotics
Structured comment name - spikein_antibiotic
Definition - Antimicrobials used in research study to assess effects of exposure on microbiome of a specific site.  Please list antimicrobial, common name and/or class and concentration used for spike-in.
Expected value - drug name; concentration
Value syntax - {text} {integer}
Example - Tetracycline at 5 mg/ml
Term ID - MIXS:0001171
Package(s) - Food
Term name - spike-in with heavy metals
Structured comment name - spikein_metal
Definition - Heavy metals used in research study to assess effects of exposure on microbiome of a specific site.  Please list heavy metals and concentration used for spike-in.
Expected value - heavy metal name or chemical symbol; concentration
Value syntax - {text} {integer}
Example - Cd at 20 ppm
Term ID - MIXS:0001172
Package(s) - Food
Term name - timepoint
Structured comment name - timepoint
Definition - Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. Indicate the timepoint written in ISO 8601 format.
Expected value - duration
Value syntax - {float}
Example - P24H
Term ID - MIXS:0001173
Package(s) - Food
Term name - water delivery frequency
Structured comment name - water_frequency
Definition - Number of water delivery events within a given period of time.
Expected value - rate
Value syntax - {float}{unit}
Example - 2 per day
Term ID - MIXS:0001174
Package(s) - Food
Term name - water source shared
Structured comment name - water_source_shared
Definition - Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes.
Expected value - enumeration
Value syntax - [multiple users, agricutural|multiple users, other|no sharing]
Example - no sharing
Term ID - MIXS:0001176
Package(s) - Food
Term name - enrichment protocol
Structured comment name - enrichment_protocol
Definition - The microbiological workflow or protocol followed to test for the presence of the target microbial analyte(s).  Please provide a PubMed or DOI reference for published protocols.
Expected value - PMID,DOI,url or free text
Value syntax - {PMID}|{DOI}|{URL}|{text}
Example - BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria
Term ID - MIXS:0001177
Package(s) - Food
Term name - food quality date
Structured comment name - food_quality_date
Definition - The date recommended for the use of the product while at peak quality, this date is not a reflection of safety unless used on infant formula this date is not a reflection of safety and is typically labeled on a food product as best if used by, best by, use by, or freeze by.
Expected value - enumeration, date
Value syntax - [best by|best if used by|freeze by||use by]; date
Example - best by 2020-05-24
Term ID - MIXS:0001178
Package(s) - Food
Term name - Interagency Food Safety Analytics Collaboration (IFSAC) category
Structured comment name - IFSAC_category
Definition - The IFSAC food categorization scheme has five distinct levels to which foods can be assigned, depending upon the type of food. First, foods are assigned to one of four food groups (aquatic animals, land animals, plants, and other). Food groups include increasingly specific food categories; dairy, eggs, meat and poultry, and game are in the land animal food group, and the category meat and poultry is further subdivided into more specific categories of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry). Finally, foods are differentiated by differences in food processing (such as pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized solid and semi-solid dairy products, and unpasteurized solid and semi-solid dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html PMID: 28926300.
Expected value - IFSAC term
Value syntax - {text}
Example - Plants:Produce:Vegetables:Herbs:Dried Herbs
Term ID - MIXS:0001179
Package(s) - Food
Term name - animal housing system
Structured comment name - animal_housing
Definition - Description of the housing system of the livestock. This field accepts terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605).
Expected value - EOL:0001605
Value syntax - {termLabel} {[termID]}
Example - pen rearing system [EOL:0001636]
Term ID - MIXS:0001180
Package(s) - Food
Term name - culture isolation date
Structured comment name - cult_isol_date
Definition - A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies.
Expected value - date and time
Value syntax - {timestamp}
Example - 2018-05-11T10:00:00+01:00
Term ID - MIXS:0001181
Package(s) - Food
Term name - food cleaning process
Structured comment name - food_clean_proc
Definition - The process of cleaning food to separate other environmental materials from the food source. Multiple terms can be separated by pipes.
Expected value - enumeration
Value syntax - [drum and drain|manual spinner|rinsed with sanitizer solution|rinsed with water|scrubbed with brush|scrubbed with hand|soaking]
Example - rinsed with water|scrubbed with brush
Term ID - MIXS:0001182
Package(s) - Food
Term name - collection site geographic feature
Structured comment name - coll_site_geo_feat
Definition - Text or terms that describe the geographic feature where the food sample was obtained by the researcher. This field accepts selected terms listed under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002), for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011} or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002]; or human construction (http://purl.obolibrary.org/obo/ENVO_00000070).
Expected value - ENVO:00000002 or ENVO:00000070
Value syntax - {text}|{termLabel} {[termID]}
Example - grocery store [ENVO:01000984]
Term ID - MIXS:0001183
Package(s) - Food
Term name - food product type
Structured comment name - food_product_type
Definition - A food product type is a class of food products that is differentiated by its food composition (e.g., single- or multi-ingredient), processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. This field accepts terms under food product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes.
Expected value - FOODON:00001002 or FOODON:03309997
Value syntax - {text}|{termLabel} {[termID]}
Example - shrimp (peeled, deep-frozen) [FOODON:03317171]
Term ID - MIXS:0001184
Package(s) - Food
Term name - fermentation chemical additives
Structured comment name - ferm_chem_add
Definition - Any chemicals that are added to the fermentation process to achieve the desired final product.
Expected value - chemical ingredient
Value syntax - {float} {unit}
Example - salt
Term ID - MIXS:0001185
Package(s) - Food
Term name - fermentation chemical additives percentage
Structured comment name - ferm_chem_add_perc
Definition - The amount of chemical added to the fermentation process.
Expected value - value
Value syntax - {float} percentage
Example - 0.01
Term ID - MIXS:0001186
Package(s) - Food
Term name - fermentation headspace oxygen
Structured comment name - ferm_headspace_oxy
Definition - The amount of headspace oxygen in a fermentation vessel.
Expected value - value
Value syntax - {float} percentage
Example - 0.05
Term ID - MIXS:0001187
Package(s) - Food
Term name - fermentation medium
Structured comment name - ferm_medium
Definition - The growth medium used for the fermented food fermentation process, which supplies the required nutrients.  Usually this includes a carbon and nitrogen source, water, micronutrients and chemical additives.
Expected value - growth medium
Value syntax - {text}
Example - molasses
Term ID - MIXS:0001188
Package(s) - Food
Term name - fermentation pH
Structured comment name - ferm_pH
Definition - The pH of the fermented food fermentation process.
Expected value - measurement value
Value syntax - {float}
Example - 4.5
Term ID - MIXS:0001189
Package(s) - Food
Term name - fermentation relative humidity
Structured comment name - ferm_rel_humidity
Definition - The relative humidity of the fermented food fermentation process.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 95% RH
Term ID - MIXS:0001190
Package(s) - Food
Term name - fermentation temperature
Structured comment name - ferm_temp
Definition - The temperature of the fermented food fermentation process.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 22 degrees Celsius
Term ID - MIXS:0001191
Package(s) - Food
Term name - fermentation time
Structured comment name - ferm_time
Definition - The time duration of the fermented food fermentation process.
Expected value - duration
Value syntax - {duration}
Example - P10D
Term ID - MIXS:0001192
Package(s) - Food
Term name - fermentation vessel
Structured comment name - ferm_vessel
Definition - The type of vessel used for containment of the fermentation.
Expected value - text
Value syntax - {text}
Example - steel drum
Term ID - MIXS:0001193
Package(s) - Food
Term name - bacteria density
Structured comment name - bacterial_density
Definition - Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043).
Expected value - measurement value
Value syntax - {float} {unit}
Example - 10 colony forming units per gram dry weight
Term ID - MIXS:0001194
Package(s) - Food
Term name - food stored by consumer (storage duration)
Structured comment name - cons_food_stor_dur
Definition - The storage duration of the food commodity by the consumer, prior to onset of illness or sample collection.  Indicate the timepoint written in ISO 8601 format.
Expected value - duration
Value syntax - {duration}
Example - P5D
Term ID - MIXS:0001195
Package(s) - Food
Term name - food stored by consumer (storage temperature)
Structured comment name - cons_food_stor_temp
Definition - Temperature at which food commodity was stored by the consumer, prior to onset of illness or sample collection.
Expected value - text or measurement value
Value syntax - {float} {unit}|{text}
Example - 4 degree Celsius
Term ID - MIXS:0001196
Package(s) - Food
Term name - purchase date
Structured comment name - cons_purch_date
Definition - The date a food product was purchased by consumer.
Expected value - date and time
Value syntax - {timestamp}
Example - 43799
Term ID - MIXS:0001197
Package(s) - Food
Term name - quantity purchased
Structured comment name - cons_qty_purchased
Definition - The quantity of food purchased by consumer.
Expected value - measurement value
Value syntax - {integer} {unit}
Example - 5 cans
Term ID - MIXS:0001198
Package(s) - Food
Term name - dietary claim or use
Structured comment name - dietary_claim_use
Definition - These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the most prominent dietary claim or use.
Expected value - FOODON:03510023
Value syntax - {text}|{termLabel} {[termID]}
Example - No preservatives [FOODON:03510113]
Term ID - MIXS:0001199
Package(s) - Food
Term name - food additive
Structured comment name - food_additive
Definition - A substance or substances added to food to maintain or improve safety and freshness, to improve or maintain nutritional value, or improve taste, texture and appearance.  This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the top 5 ingredients listed in order as on the food label.  See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors.
Expected value - FOODON:03412972
Value syntax - {text}|{termLabel} {[termID]}
Example - xanthan gum [FOODON:03413321]
Term ID - MIXS:0001200
Package(s) - Food
Term name - food allergen labeling
Structured comment name - food_allergen_label
Definition - A label indication that the product contains a recognized allergen. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213).
Expected value - FOODON:03510213
Value syntax - {text}|{termLabel} {[termID]}
Example - food allergen labelling about crustaceans and products thereof [FOODON:03510215]
Term ID - MIXS:0001201
Package(s) - Food
Term name - food cooking process
Structured comment name - food_cooking_proc
Definition - The transformation of raw food by the application of heat. This field accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002).
Expected value - FOODON:03450002
Value syntax - {text}|{termLabel} {[termID]}
Example - food blanching [FOODON:03470175]
Term ID - MIXS:0001202
Package(s) - Food
Term name - food distribution point geographic location
Structured comment name - food_dis_point
Definition - A reference to a place on the Earth, by its name or by its geographical location that refers to a distribution point along the food chain. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012.
Expected value - country: region, specific location
Value syntax - {term}: {term}, {text}
Example - USA: Delmarva, Peninsula
Term ID - MIXS:0001203
Package(s) - Food
Term name - food distribution point geographic location (city)
Structured comment name - food_dis_point_city
Definition - A reference to a place on the Earth, by its name or by its geographical location that refers to a distribution point along the food chain. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012.
Expected value - GAZ:00000448
Value syntax - {text}|{termLabel} {[termID]}
Example - Atlanta[GAZ:00004445]
Term ID - MIXS:0001204
Package(s) - Food
Term name - food ingredient
Structured comment name - food_ingredient
Definition - In this field, please list individual ingredients for multi-component food [FOODON:00002501] and simple foods that is not captured in food_type.  Please use terms that are present in FoodOn.  Multiple terms can be separated by one or more pipes |, but please consider limiting this list to the top 5 ingredients listed in order as on the food label.  See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors.
Expected value - FOODON
Value syntax - {text}|{termLabel} {[termID]}
Example - bean (whole) [FOODON:00002753]
Term ID - MIXS:0001205
Package(s) - Food
Term name - food product name legal status
Structured comment name - food_name_status
Definition - A datum indicating that use of a food product name is regulated in some legal jurisdiction. This field accepts terms listed under food product name legal status (http://purl.obolibrary.org/obo/FOODON_03530087).
Expected value - FOODON:03530087
Value syntax - {termLabel} {[termID]}
Example - protected geographic indication [FOODON:03530256]
Term ID - MIXS:0001206
Package(s) - Food
Term name - food product origin geographic location
Structured comment name - food_origin
Definition - A reference to a place on the Earth, by its name or by its geographical location that describes the origin of the food commodity, either in terms of its cultivation or production. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448).
Expected value - country: region, specific location
Value syntax - {term}: {term}, {text}
Example - USA: Delmarva, Peninsula
Term ID - MIXS:0001207
Package(s) - Food
Term name - food package capacity
Structured comment name - food_pack_capacity
Definition - The maximum number of product units within a package
Expected value - measurement value
Value syntax - {float} {unit}
Example - 454 grams
Term ID - MIXS:0001208
Package(s) - Food
Term name - food packing medium integrity
Structured comment name - food_pack_integrity
Definition - A term label and term id to describe the state of the packing material and text to explain the exact condition.  This field accepts terms listed under food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218).
Expected value - FOODON:03530218
Value syntax - {text}|{termLabel} {[termID]}
Example - food packing medium compromised [FOODON:00002517]
Term ID - MIXS:0001209
Package(s) - Food
Term name - material of contact prior to food packaging
Structured comment name - food_prior_contact
Definition - The material the food contacted (e.g., was processed in) prior to packaging. This field accepts terms listed under material of contact prior to food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper descriptor is not listed please use text to describe the material of contact prior to food packaging.
Expected value - FOODON:03530077
Value syntax - {text}|{termLabel} {[termID]}
Example - processed in stainless steel container [FOODON:03530081]
Term ID - MIXS:0001210
Package(s) - Food
Term name - food production system characteristics
Structured comment name - food_prod
Definition - Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef,  domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes.
Expected value - FOODON:03530206
Value syntax - {termLabel} {[termID]}
Example - organic plant cultivation [FOODON:03530253]
Term ID - MIXS:0001211
Package(s) - Food
Term name - food product synonym
Structured comment name - food_prod_synonym
Definition - Other names by which the food product is known by (e.g., regional or non-English names).
Expected value - text
Value syntax - {text}
Example - pinot gris
Term ID - MIXS:0001212
Package(s) - Food
Term name - food product by quality
Structured comment name - food_product_qual
Definition - Descriptors for describing food visually or via other senses, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like food (frozen) are both a quality descriptor and the output of a process. This field accepts terms listed under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454).
Expected value - FOODON:00002454
Value syntax - {termLabel} {[termID]}
Example - raw [FOODON:03311126]
Term ID - MIXS:0001213
Package(s) - Food
Term name - food traceability list category
Structured comment name - food_trace_list
Definition - The FDA is proposing to establish additional traceability recordkeeping requirements (beyond what is already required in existing regulations) for persons who manufacture, process, pack, or hold foods the Agency has designated for inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies the foods for which the additional traceability records described in the proposed rule would be required. The term “Food Traceability List” (FTL) refers not only to the foods specifically listed (https://www.fda.gov/media/142303/download), but also to any foods that contain listed foods as ingredients.
Expected value - enumeration
Value syntax - [cheeses-other than hard cheeses|cucumbers|crustaceans|finfish-including smoked finfish|fruits and vegetables-fresh cut|herbs-fresh|leafy greens-including fresh cut leafy greens|melons|mollusks-bivalves|nut butter|peppers|ready to eat deli salads|sprouts|tomatoes|tropical tree fruits|shell eggs]
Example - tropical tree fruits
Term ID - MIXS:0001214
Package(s) - Food
Term name - Hazard Analysis Critical Control Points (HACCP) guide food safety term
Structured comment name - HACCP_term
Definition - Hazard Analysis Critical Control Points (HACCP) food safety terms; This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221).
Expected value - FOODON:03530221
Value syntax - {termLabel} {[termID]}
Example - tetrodotoxic poisoning [FOODON:03530249]
Term ID - MIXS:0001215
Package(s) - Food
Term name - microbiological culture medium
Structured comment name - microb_cult_med
Definition - A culture medium used to select for, grow, and maintain prokaryotic microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) forms. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the culture medium.
Expected value - MICRO:0000067
Value syntax - {text}|{termLabel} {[termID]}
Example - brain heart infusion agar [MICRO:0000566]
Term ID - MIXS:0001216
Package(s) - Food
Term name - microbial starter
Structured comment name - microb_start
Definition - Any type of microorganisms used in food production.  This field accepts terms listed under live organisms for food production (http://purl.obolibrary.org/obo/FOODON_0344453).
Expected value - FOODON:03544453
Value syntax - {term label} {[termID]}|{text}
Example - starter cultures [FOODON:03544454]
Term ID - MIXS:0001217
Package(s) - Food
Term name - microbial starter organism count
Structured comment name - microb_start_count
Definition - Total cell count of starter culture per gram, volume or area of sample and the method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided. (example : total prokaryotes; 3.5e7 cells per ml; qPCR).
Expected value - organism name; measurement value; enumeration
Value syntax - {text};{float} {unit};[ATP|MPN|qPCR|spread plate|other]
Example - total prokaryotes;3.5e9 colony forming units per milliliter;spread plate
Term ID - MIXS:0001218
Package(s) - Food
Term name - microbial starter inoculation
Structured comment name - microb_start_inoc
Definition - The amount of starter culture used to inoculate a new batch.
Expected value - measurement
Value syntax - {float} {unit}
Example - 100 milligrams
Term ID - MIXS:0001219
Package(s) - Food
Term name - microbial starter preparation
Structured comment name - microb_start_prep
Definition - Information about the protocol or method used to prepare the starter inoculum.
Expected value - text
Value syntax - {text}
Example - liquid starter culture, propagated 3 cycles in milk prior to inoculation
Term ID - MIXS:0001220
Package(s) - Food
Term name - microbial starter source
Structured comment name - microb_start_source
Definition - The source from which the microbial starter culture was sourced.  If commercially supplied, list supplier.
Expected value - text
Value syntax - {text}
Example - backslopped, GetCulture
Term ID - MIXS:0001221
Package(s) - Food
Term name - microbial starter NCBI taxonomy ID
Structured comment name - microb_start_taxID
Definition - Please include Genus species and strain ID, if known of microorganisms used in food production. For complex communities, pipes can be used to separate two or more microbes.
Expected value - NCIT:C14250 or NCBI taxid
Value syntax - {termLabel} {[termID]}|{integer}
Example - Lactobacillus rhamnosus [NCIT:C123495]
Term ID - MIXS:0001222
Package(s) - Food
Term name - nucleic acid extraction kit
Structured comment name - nucl_acid_ext_kit
Definition - The name of the extraction kit used to recover the nucleic acid fraction of an input material is performed.
Expected value - The name of an extraction kit
Value syntax - {text}
Example - Qiagen PowerSoil Kit
Term ID - MIXS:0001223
Package(s) - Food
Term name - number of samples collected
Structured comment name - num_samp_collect
Definition - The number of samples collected during the current sampling event.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 116 samples
Term ID - MIXS:0001224
Package(s) - Food
Term name - sample collection method
Structured comment name - sample_collec_method
Definition - The method employed for collecting the sample.
Expected value - PMID,DOI,url , or text
Value syntax - {PMID}|{DOI}|{URL}|{text}
Example - environmental swab sampling
Term ID - MIXS:0001225
Package(s) - Food (& add to core)
Term name - biological sample replicate
Structured comment name - samp_rep_biol
Definition - Measurements of biologically distinct samples that show biological variation.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 6 replicates
Term ID - MIXS:0001226
Package(s) - Food

see discussion onn replicate samples #26

Term name - technical sample replicate
Structured comment name - samp_rep_tech
Definition - Repeated measurements of the same sample that show independent measures of the noise associated with the equipment and the protocols.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 10 replicates
Term ID - MIXS:0001227
Package(s) - Food

see discussion onn replicate samples #26

Term name - sample storage device
Structured comment name - samp_stor_device
Definition - The container used to store the  sample. This field accepts terms listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the proper descriptor is not listed please use text to describe the storage device.
Expected value - NCIT:C4318
Value syntax - {text}|{termLabel} {[termID]}
Example - Whirl Pak sampling bag [GENEPIO:0002122]
Term ID - MIXS:0001228
Package(s) - Food
Term name - sample storage media
Structured comment name - samp_stor_media
Definition - The liquid that is added to the sample collection device prior to sampling. If the sample is pre-hydrated, indicate the liquid media the sample is pre-hydrated with for storage purposes. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the sample storage media.
Expected value - MICRO:0000067
Value syntax - {text}|{termLabel} {[termID]}
Example - peptone water medium [MICRO:0000548]
Term ID - MIXS:0001229
Package(s) - Food
Term name - sample transport  container
Structured comment name - samp_transport_cont
Definition - Conatiner in which the sample was stored during transport. Indicate the location name.
Expected value - enumeration
Value syntax - [bottle|cooler|glass vial|plastic vial||vendor supplied container]
Example - cooler
Term ID - MIXS:0001230
Package(s) - Food
Term name - sample transport duration
Structured comment name - samp_transport_dur
Definition - The duration of time from when the sample was collected until processed. Indicate the duration for which the sample was stored written in ISO 8601 format.
Expected value - measurement value
Value syntax - {float} {unit}
Example - P10D
Term ID - MIXS:0001231
Package(s) - Food
Term name - sample transport temperature
Structured comment name - samp_transport_temp
Definition - Temperature at which sample was transported, e.g. -20 or 4 degree Celsius.
Expected value - text or measurement value
Value syntax - {float} {unit} {text}
Example - 4 degree Celsius
Term ID - MIXS:0001232
Package(s) - Food
Term name - specific intended consumer
Structured comment name - spec_intended_cons
Definition - Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136).
Expected value - FOODON:03510136
Value syntax - {termLabel} {[termID]}
Example - senior as food consumer [FOODON:03510254]
Term ID - MIXS:0001234
Package(s) - Food

How is this different to "intended consumer" [MIXS:0001144] proposed above?

Term name - antimicrobial phenotype of spike-in bacteria
Structured comment name - spikein_AMR
Definition - Qualitative description of a microbial response to antimicrobial agents. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases. This field accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299).
Expected value - measurement value ARO:3004299
Value syntax - {float} {unit};{termLabel} {[termID]}
Example - wild type [ARO:3004432]
Term ID - MIXS:0001235
Package(s) - Food
Term name - study design
Structured comment name - study_design
Definition - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. This field accepts terms under study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor is not listed please use text to describe the study design. Multiple terms can be separated by pipes.
Expected value - OBI:0500000
Value syntax - {text}|{termLabel} {[termID]}
Example - in vitro design [OBI:0001285]
Term ID - MIXS:0001236
Package(s) - Food
Term name - study incubation duration
Structured comment name - study_inc_dur
Definition - Sample incubation duration if unpublished or unvalidated method is used. Indicate the timepoint written in ISO 8601 format.
Expected value - duration
Value syntax - {float} {unit}
Example - P24H
Term ID - MIXS:0001237
Package(s) - Food
Term name - study incubation temperature
Structured comment name - study_inc_temp
Definition - Sample incubation temperature if unpublished or unvalidated method is used.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 37 degree Celsius
Term ID - MIXS:0001238
Package(s) - Food
Term name - time-course duration
Structured comment name - study_timecourse
Definition - For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study.
Expected value - measurement value
Value syntax - {float} {unit}
Example - 2 days post inoculation
Term ID - MIXS:0001239
Package(s) - Food
Term name - study treatment
Structured comment name - study_tmnt
Definition - A process in which the act is intended to modify or alter some other material entity.  From the study design, each treatment is comprised of one level of one or multiple factors. This field accepts terms listed under treatment (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not listed please use text to describe the study treatment. Multiple terms can be separated by one or more pipes.
Expected value - MCO:0000866
Value syntax - {text}|{termLabel} {[termID]}
Example - Factor A|spike-in|levels high, medium, low
Term ID - MIXS:0001240
Package(s) - Food
Term name - food animal antimicrobial
Structured comment name - animal_am
Definition - The drug class(es) or name(s) (generic or brand) of the antimicrobial(s) given to the food animal within the last 30 days.
Expected value - text
Value syntax - {text}
Example - tetracycline
Term ID - MIXS:0001243
Package(s) - Food
Term name - food animal antimicrobial duration
Structured comment name - animal_am_dur
Definition - The duration of time (days) that the antimicrobial was administered to the food animal.
Expected value - value
Value syntax - {float} {day}
Example - 3 days
Term ID - MIXS:0001244
Package(s) - Food
Term name - food animal antimicrobial frequency
Structured comment name - animal_am_freq
Definition - The frequency per day that the antimicrobial was adminstered to the food animal.
Expected value - value
Value syntax - {float} {unit}
Example - once daily
Term ID - MIXS:0001245
Package(s) - Food
Term name - food animal antimicrobial route of administration
Structured comment name - animal_am_route
Definition - The route by which the antimicrobial is adminstered into the body of the food animal.
Expected value - text
Value syntax - {text}
Example - oral-feed
Term ID - MIXS:0001246
Package(s) - Food
Term name - food animal antimicrobial intended use
Structured comment name - animal_am_use
Definition - The prescribed intended use of or the condition treated by the antimicrobial given to the food animal by any route of administration.
Expected value - text
Value syntax - {text}
Example - shipping fever
Term ID - MIXS:0001247
Package(s) - Food
Term name - food animal body condition
Structured comment name - animal_body_cond
Definition - Body condition scoring is a production management tool used to evaluate overall health and nutritional needs of a food animal. Because there are different scoring systems, this field is restricted to three categories.
Expected value - enumeration
Value syntax - [normal|over conditioned|under conditioned]
Example - under conditioned
Term ID - MIXS:0001248
Package(s) - Food
Term name - food animal source sex category
Structured comment name - animal_sex
Definition - The sex and reproductive status of the food animal.
Expected value - enumeration
Value syntax - [castrated female|castrated male|intact female|intact male]
Example - castrated male
Term ID - MIXS:0001249
Package(s) - Food
Term name - environmental feature
Structured comment name - env_feature
Definition - Add terms that identify any adjunct characteristics of the environmental setting of the food commodity that was investigated. This includes characteristics such as geographic feature, water body, plant feed, animal feed, climatic zone, etc.. This field accepts terms listed under environmental feature (http://purl.obolibrary.org/obo/ENVO_00002297) as implemented in FoodOn.  Multiple terms can be separated by one or more pipes.
Expected value - ENVO:00002297
Value syntax - {text}|{termLabel} {[termID]}
Example - food processing building [ENVO:00003863]|animal feed [ENVO:02000047]
Term ID - MIXS:0001250
Package(s) - Food

Isn't this "env_loc_scale" ?

Term name - food source age
Structured comment name - food_source_age
Definition - The age of the food source host organim. Depending on the type of host organism, age may be more appropriate to report in days, weeks, or years.
Expected value - value
Value syntax - {float} {unit}
Example - P6M
Term ID - MIXS:0001251
Package(s) - Food
Term name - facility type
Structured comment name - facility_type
Definition - Establishment details about the type of facility where the sample was taken. This is independent of the specific product(s) within the facility.
Expected value - enumeration
Value syntax - [ambient storage|caterer-catering point|distribution|frozen storage|importer-broker|interstate conveyance|labeler-relabeler|manufacturing-processing|packaging|refrigerated storage|storage]
Example - manufacturing-processing
Term ID - MIXS:0001252
Package(s) - Food
Term name - hygienic food production area
Structured comment name - hygienic_area
Definition - The subdivision of areas within a food production facility according to hygienic requirements. This field accepts terms listed under hygienic food production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that most accurately indicates the hygienic area your sample was taken from according to the definitions provided.
Expected value - ENVO
Value syntax - {termLabel} {[termID]}
Example - Low Hygiene Area
Term ID - MIXS:0001253
Package(s) - Food
Term name - food production environmental monitoring zone
Structured comment name - env_monitoring_zone
Definition - An environmental monitoring zone is a formal designation as part of an environmental monitoring program, in which areas of a food production facility are categorized, commonly as zones 1-4, based on likelihood or risk of foodborne pathogen contamination. This field accepts terms listed under food production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO). Please add a term to indicate the environmental monitoring zone the sample was taken from.
Expected value - ENVO
Value syntax - {termLabel} {[termID]}
Example - Zone 1
Term ID - MIXS:0001254
Package(s) - Food
Term name - area sampled size
Structured comment name - area_samp_size
Definition - The size of the area that was sampled. This field accepts measurement values. The submitter should choose the appropriate level of information to disclose based on institutional practices and privacy considerations.
Expected value - measurement value
Value syntax - {integer} {unit} x {integer} {unit}
Example - 12 centimeter x 12 centimeter
Term ID - MIXS:0001255
Package(s) - Food
Term name - sample surface moisture
Structured comment name - samp_surf_moisture
Definition - Degree of water held on a sampled surface.  If present, user can state the degree of water held on surface (intermittent moisture, submerged). If no surface moisture is present indicate not present.
Expected value - enumeration
Value syntax - [intermittent moisture|not present|submerged]
Example - submerged
Term ID - MIXS:0001256
Package(s) - Food
Term name - sample location condition
Structured comment name - samp_loc_condition
Definition - The condition of the sample location at the time of sampling.
Expected value - enumeration
Value syntax - [damaged|new|rupture|visible signs of mold-mildew|visible weariness repair]
Example - new
Term ID - MIXS:0001257
Package(s) - Food
Term name - biocide
Structured comment name - biocide_used
Definition - Substance intended for preventing, neutralizing, destroying, repelling, or mitigating the effects of any pest or microorganism; that inhibits the growth, reproduction, and activity of organisms, including fungal cells; decreases the number of fungi or pests present; deters microbial growth and degradation of other ingredients in the formulation. Indicate the biocide used on the location where the sample was taken. Multiple terms can be separated by pipes.
Expected value - commercial name of biocide, active ingredient in biocide or class of biocide
Value syntax - {text}
Example - Quaternary ammonium compound|SterBac
Term ID - MIXS:0001258
Package(s) - Food
Term name - sampling room sterilization method
Structured comment name - ster_meth_samp_room
Definition - The method used to sterilize the sampling room. This field accepts terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026). If the proper descriptor is not listed, please use text to describe the sampling room sterilization method. Multiple terms can be separated by pipes.
Expected value - ENVO:01001026
Value syntax - {text}|{termLabel} {[termID]}
Example - ultraviolet radiation [ENVO:21001216]|infrared radiation [ENVO:21001214]
Term ID - MIXS:0001259
Package(s) - Food
only1chunts commented 3 years ago

The term "env_feature" was replaced with "env_local_scale" so this term is not being created again here:

Term name - environmental feature
Structured comment name - env_feature
Definition - Add terms that identify any adjunct characteristics of the environmental setting of the food commodity that was investigated. This includes characteristics such as geographic feature, water body, plant feed, animal feed, climatic zone, etc.. This field accepts terms listed under environmental feature (http://purl.obolibrary.org/obo/ENVO_00002297) as implemented in FoodOn.  Multiple terms can be separated by one or more pipes.
Expected value - ENVO:00002297
Value syntax - {text}|{termLabel} {[termID]}
Example - food processing building [ENVO:00003863]|animal feed [ENVO:02000047]
Term ID - MIXS:0001250
Package(s) - Food